On a roll for new TRF targets

doi:10.1101/GAD.1623207

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Journal Article•DOI•

Regulation of gene expression via the core promoter and the basal transcriptional machinery.

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Tamar Juven-Gershon¹, James T. Kadonaga¹•Institutions (1)

University of California, San Diego¹

15 Mar 2010-Developmental Biology

TL;DR: The findings suggest that the core promoter and basal transcription factors are important yet mostly unexplored components in the regulation of gene expression.

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489 citations

Cites background from "On a roll for new TRF targets"

...This concept is nicely exemplified in studies of the TBP-related factors (TRFs) (for reviews, see: Jones, 2007; Müller et al., 2007; Reina and Hernandez, 2007; Torres-Padilla and Tora, 2007)....
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Journal Article•DOI•

The RNA Polymerase II Core Promoter – the Gateway to Transcription

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Tamar Juven-Gershon¹, Jer-Yuan Hsu¹, Joshua W. M. Theisen¹, James T. Kadonaga¹•Institutions (1)

University of California, San Diego¹

01 Jun 2008-Current Opinion in Cell Biology

TL;DR: The core promoter is a sophisticated gateway to transcription that determines which signals will lead to transcription initiation and may contain many different sequence motifs that specify different mechanisms of transcription and responses to enhancers.

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380 citations

Journal Article•DOI•

The basal initiation machinery: beyond the general transcription factors.

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Timothy W. Sikorski¹, Stephen Buratowski¹•Institutions (1)

Harvard University¹

01 Jun 2009-Current Opinion in Cell Biology

TL;DR: A simple model in which basal transcription factors sequentially assembled with RNA Polymerase II to generate a preinitiation complex (PIC) indicates that PIC composition is not universal, but promoter-dependent.

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193 citations

Cites background from "On a roll for new TRF targets"

...The other subunits of TFIID (the TBP-associated factors or TAFs) appear to interact with INR and DPEs....
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...Leurent C, Sanders S, Ruhlmann C, Mallouh V, Weil PA, Kirschner DB, Tora L, Schultz P: Mapping histone fold TAFs within yeast TFIID....
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...In higher eukaryotes, there are multiple genes encoding TBP-related factors (TRFs) and variant TAFs [1,7]....
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Journal Article•DOI•

The core promoter: At the heart of gene expression.

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Yehuda M. Danino¹, Dan Y. Even¹, Diana Ideses¹, Tamar Juven-Gershon¹•Institutions (1)

Bar-Ilan University¹

01 Aug 2015-Biochimica et Biophysica Acta

TL;DR: A broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression are reviewed and future research directions and challenges are suggested.

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140 citations

Cites background from "On a roll for new TRF targets"

...which is essential for interaction with the TATA box (reviewed in [121-123, 144-146]....
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Journal Article•DOI•

Developmental regulation of transcription initiation: more than just changing the actors.

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Ferenc Müller¹, Andreas Zaucker¹, Laszlo Tora²•Institutions (2)

University of Birmingham¹, French Institute of Health and Medical Research²

01 Oct 2010-Current Opinion in Genetics & Development

TL;DR: The proposed models of transcription initiation by alternative initiation complexes in distinct stages of developmental specialization during vertebrate ontogeny are summarized.

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83 citations

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Journal Article•DOI•

Metazoan replication-dependent histone mRNAs: a distinct set of RNA polymerase II transcripts

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William F. Marzluff¹•Institutions (1)

University of North Carolina at Chapel Hill¹

01 Jun 2005-Current Opinion in Cell Biology

TL;DR: Metazoan replication-dependent histone mRNAs are the only eukaryotic m RNAs that lack polyA tails and several novel factors, including components of the U7 snRNP, as well as proteins involved in regulation of histone gene expression have been described.

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144 citations

"On a roll for new TRF targets" refers background in this paper

...Rather, they terminate with a well-conserved stem-andloop structure that regulates their maturation, translation, and stability (Marzluff 2005)....
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Journal Article•DOI•

Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters

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Laura Schramm¹, P. Shannon Pendergrast, Yuling Sun, Nouria Hernandez•Institutions (1)

Stony Brook University¹

15 Oct 2000-Genes & Development

TL;DR: Two novel activities are characterized, a human homolog of yeast B, which is required for transcription of both TATA-less and snRNA-type RNA polymerase III promoters, and a factor equally related to human BRF and TFIIB, designated BRFU,Which is specifically required forcription of sn RNA- type RNA polymerases III promoters.

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Abstract: Correct initiation of transcription by RNA polymerase III requires a number of factors. Of particular interest is the transcription factor IIIB (TFIIIB), because TFIIIB directly contacts RNA polymerase III, and in yeast, once recruited to the promoter, TFIIIB is sufficient to support several rounds of RNA polymerase III transcription (reviewed in Paule and White 2000). Yeast TFIIIB is well defined and consists of three subunits, the TATA box–binding protein TBP (Kassavetis et al. 1992), the TFIIB-related factor BRF (TDS4/PCF4) (Buratowski and Zhou 1992; Colbert and Hahn 1992; Lopez-De-Leon et al. 1992), and the B′′ protein (TFIIIB90/TFC5/TFC7) (Kassavetis et al. 1995; Roberts et al. 1996; Ruth et al. 1996). In various RNA polymerase III promoters, the mode of TFIIIB recruitment varies. In the gene-internal 5S and transfer RNA (tRNA) promoters, the promoter elements are first recognized by TFIIIA and TFIIIC or directly by TFIIIC, respectively, and this allows the subsequent recruitment of TFIIIB (reviewed in Paule and White 2000). On the yeast U6 promoter, which contains a TATA box ∼25 nucleotides upstream of the transcription start site, TFIIIB is also recruited in a TFIIIC-dependent manner (Brow and Guthrie 1990; Burnol et al. 1993; Eschenlauer et al. 1993), but on naked DNA templates in vitro, it can be recruited by direct binding of the TBP subunit to the TATA box (Moenne et al. 1990; Margottin et al. 1991). In all these cases, however, the same TFIIIB complex, containing the same three subunits, is used (Joazeiro et al. 1994). In mammalian cells, the situation appears more complicated. Like yeast TFIIIB, mammalian TFIIIB contains TBP (Lobo et al. 1992; Taggart et al. 1992; White and Jackson 1992) and a homolog of yeast BRF, human BRF (hBRF) (Mital et al. 1996), also called TFIIIB90 (Wang and Roeder 1995). These two subunits associate strongly with each other (Wang and Roeder 1995; Mital et al. 1996). A homolog of yeast B′′ has not been identified in mammals or any other organism. In addition, unlike in yeast, there appear to be variants of the TFIIIB complex. In particular, the human U6 promoter, which exemplifies a class of RNA polymerase III promoters whose essential elements are all located within the 5′ flanking sequence of the gene, appears to use another form of TFIIIB than the tRNA-type Ad2 VAI promoter (Lobo et al. 1992; Teichmann and Seifart 1995; Mital et al. 1996; Henry et al. 1998a), which contains a gene-internal promoter. The core U6 promoter, which is sufficient to direct basal levels of transcription in vitro, consists of a proximal sequence element (PSE) centered around position −56 relative to the start site and a TATA box centered around position −27. The U6 promoter is highly similar to the RNA polymerase II small nuclear RNA (snRNA) core promoters, which consist of only the PSE (see Henry et al. 1998a and references therein). The PSE recruits a multisubunit complex called SNAPc (Henry et al. 1995, 1998b) or PTF (Yoon et al. 1995), and the U6 TATA box recruits TBP (Lobo et al. 1991; Simmen et al. 1991). It is not clear which other TFIIIB components aside from TBP are involved in U6 transcription. Wang and Roeder (1995) showed that depletion of extracts with anti-hBRF antibodies debilitated U6 transcription, but addition of recombinant hBRF did not restore activity. They concluded that hBRF was required for U6 transcription but as part of a complex that somehow differed from the TFIIIB complex required for VAI transcription. On the other hand, we showed that depletion of extracts with antibodies directed against the C-terminal half of hBRF debilitated transcription from the VAI promoter but not from the U6 promoter. Because the antibody treatment removed >95% of the endogenous hBRF present in extracts, the results suggest that hBRF is in fact not required for U6 transcription (Mital et al. 1996). Indeed, we were able also show that upon depletion of extracts with anti-TBP and anti-hBRF antibodies, VAI transcription was only restored by addition of a combination of both TBP and hBRF, whereas U6 transcription could be restored by addition of only recombinant TBP. In fact, U6 transcription was diminished by addition of hBRF (Henry et al. 1998a). Thus, two main questions remain concerning mammalian TFIIIB. First, it is currently unclear whether a mammalian homolog of yeast B′′ exists, and whether it is required for RNA polymerase III transcription of genes with internal promoters, such as the VAI gene, and genes with external promoters that recruit SNAPc, such as the human U6 gene. Second, the apparent lack of requirement for hBRF in U6 transcription raises the possibility that the mammalian snRNA-type RNA polymerase III promoters use a factor different from, but related to, hBRF. Here, we report the characterization of two new transcription factors, human B′′ (hB′′) and a BRF-related factor we refer to as hBRFU. hB′′ is required for transcription of both the VAI and the U6 genes. hBRFU is a protein with an N-terminal domain related to both hBRF and TFIIB, and a divergent C-terminal domain. The protein is required for U6 but not VAI transcription. These results show that there are two forms of the basal RNA polymerase III transcription factor IIIB in mammalian cells. They also identify the first transcription factors uniquely required for transcription of RNA polymerase III but not RNA polymerase II—snRNA promoters. Together with our previous results indicating that TFIIB is required for transcription of the human RNA polymerase II snRNA genes (Kuhlman et al. 1999), these results suggest that the key event in the determination of RNA polymerase specificity in the human snRNA promoters is the recruitment of hBRFU versus TFIIB.

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138 citations

"On a roll for new TRF targets" refers background in this paper

...…cells contain two TFIIIB activities involved in transcription of distinct classes of pol III genes, one corresponding to yeast TFIIIB containing human Brf1 and TBP, and a second one in which Brf1 is replaced by another TFIIB-related factor called Brf2 (Teichmann et al. 1999; Schramm et al. 2000)....
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Journal Article•DOI•

Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus.

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Gert Jan C. Veenstra¹, Daniel L. Weeks², Alan P. Wolffe³•Institutions (3)

National Institutes of Health¹, University of Iowa², Sangamo BioSciences³

22 Dec 2000-Science

TL;DR: It is found that the TBP-like factor TLF/TRF2 is essential for development past the mid-blastula stage and although similar mechanistic roles exist in common, TBP and TLF function differentially to control transcription of specific genes.

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Abstract: The TATA-binding protein (TBP) is believed to function as a key component of the general transcription machinery We tested the role of TBP during the onset of embryonic transcription by antisense oligonucleotide-mediated turnover of maternal TBP messenger RNA Embryos without detectable TBP initiated gastrulation but died before completing gastrulation The expression of many genes transcribed by RNA polymerase II and III was reduced; however, some genes were transcribed with an efficiency identical to that of TBP-containing embryos Using a similar antisense strategy, we found that the TBP-like factor TLF/TRF2 is essential for development past the mid-blastula stage Because TBP and a TLF factor play complementary roles in embryonic development, our results indicate that although similar mechanistic roles exist in common, TBP and TLF function differentially to control transcription of specific genes

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138 citations

"On a roll for new TRF targets" refers background or methods or result in this paper

...Among the three classes of TBP-related factors described so far, TRF2—also called TBP-like protein (TLP) or TBP-like factor (TLF)—is the only one to be widely present in metazoans (Ohbayashi et al. 1999; Kaltenbach et al. 2000; Veenstra et al. 2000)....
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...…was discovered by analysis of ESTs by several groups and, accordingly, variously named TRF2 (Rabenstein et al. 1999; Teichmann et al. 1999), TRF (Maldonado 1999), TLP (Ohbayashi et al. 1999, 2001), TLF (Kaltenbach et al. 2000; Veenstra et al. 2000), or TBPrelated protein (TRP) (Moore et al. 1999)....
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...This is consistent with studies in nematode, fly, fish, and frog, where inactivation of TRF2 results in a block in embryonic development and lethality (Dantonel et al. 2000; Kaltenbach et al. 2000; Veenstra et al. 2000; Bartfai et al. 2004; Kopytova et al. 2006)....
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Journal Article•DOI•

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Thomas E. Crowley¹, Timothy Hoey², Jen-Kuei Liu¹, Yuh Nung Jan¹, Lily Yeh Jan¹, Robert Tjian² - Show less +2 more•Institutions (2)

University of California, San Francisco¹, University of California, Berkeley²

11 Feb 1993-Nature

TL;DR: The cloning and characterization of a Drosophila gene product with considerable sequence similarity to TBP and a highly restricted expression pattern in the embryo suggest that TBP-related factor is a sequence-specific transcription factor that shares the DNA-binding properties of TBP.

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Abstract: The TATA-binding protein TBP is necessary for the transcription of eukaryotic genes. Multi-protein complexes formed by TBP and different TBP-associated factors are involved in the initiation of transcription by polymerases I and II, and probably III as well. During the formation of an active initiation complex, TBP makes specific contacts with other proteins, for example TFIIB and RNA polymerase II (refs 2-4). Here we describe the cloning and characterization of a Drosophila gene product with considerable sequence similarity to TBP and a highly restricted expression pattern in the embryo. This TBP-related factor is a DNA-binding protein but is not likely to be a basal transcription factor. Our results suggest that TBP-related factor is a sequence-specific transcription factor that shares the DNA-binding properties of TBP.

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130 citations

"On a roll for new TRF targets" refers background in this paper

...TRF1 has been found only in Drosophila and Anopheles (Crowley et al. 1993; Isogai et al. 2007b), and TRF3 is restricted to vertebrates (Persengiev et al. 2003)....
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...Indeed, shortly thereafter, the first TBP-related factor, TRF1, was described (Crowley et al. 1993)....
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Journal Article•DOI•

The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans embryogenesis.

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Linda S. Kaltenbach¹, Michael A. Horner¹, Joel H. Rothman², Susan E. Mango¹•Institutions (2)

Huntsman Cancer Institute¹, University of California, Santa Barbara²

01 Sep 2000-Molecular Cell

TL;DR: It is reported that CeTLF is required to express a subset of Pol II genes and associates with at least one of these genes in vivo and performs a unique function in activating Pol II transcription distinct from that of CeTBP.

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121 citations

"On a roll for new TRF targets" refers background or methods or result in this paper

...Among the three classes of TBP-related factors described so far, TRF2—also called TBP-like protein (TLP) or TBP-like factor (TLF)—is the only one to be widely present in metazoans (Ohbayashi et al. 1999; Kaltenbach et al. 2000; Veenstra et al. 2000)....
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...…was discovered by analysis of ESTs by several groups and, accordingly, variously named TRF2 (Rabenstein et al. 1999; Teichmann et al. 1999), TRF (Maldonado 1999), TLP (Ohbayashi et al. 1999, 2001), TLF (Kaltenbach et al. 2000; Veenstra et al. 2000), or TBPrelated protein (TRP) (Moore et al. 1999)....
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...TRF2 was discovered by analysis of ESTs by several groups and, accordingly, variously named TRF2 (Rabenstein et al. 1999; Teichmann et al. 1999), TRF (Maldonado 1999), TLP (Ohbayashi et al. 1999, 2001), TLF (Kaltenbach et al. 2000; Veenstra et al. 2000), or TBPrelated protein (TRP) (Moore et al. 1999)....
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...This is consistent with studies in nematode, fly, fish, and frog, where inactivation of TRF2 results in a block in embryonic development and lethality (Dantonel et al. 2000; Kaltenbach et al. 2000; Veenstra et al. 2000; Bartfai et al. 2004; Kopytova et al. 2006)....
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On a roll for new TRF targets

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